It feels like a pejorative because we used to just refer to dominant groups as ... nothing. Just a blank space where a word should be.
"In this country American means white. Everybody else has to hyphenate." – Toni Morrison
This can be applied to cisgendered people, heterosexual people, white people, and the way the blogosphere uses the term "men".
Cis, het, white, men, and even at this point the word Christian are most notoriously used in the context of pointing out how those groups have oppressed, most people don't want to see themselves as an oppressor, and thus they bristle at the terms.
You're dead-on. It's not a pejorative. It's necessary to be precise in who you're talking about--whether heaping praise, criticism, or just spitting facts.
Great piece. Surprised I haven't read someone tackle this before, but I'm glad you did. You did it well.
Signed,
A white, cis, het man (but not Christian, just a retired Catholic).